You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
To install SNPest, you first need to install the phy library as described here:
http://github.com/jakob-skou-pedersen/phy/
For SNPest to work, you have to place the 'dfgEval_SNPest.cpp' file in the '/phy/src' folder along with the modified version of the 'Makefile.am' provided with SNPest.
The folder 'dfgspec' contains all the model specifications and should be placed in the '/phy/src' folder as well.
SNPest.pl reads input on STDIN and outputs the genotype data on STDOUT.
You should use the provided script 'cleanupvcf.pl' to generate a high quality set of SNPs and indels from the output. The default is to use a minimum read depth of 10X, a minimum phred scaled quality of 30, and - for insertions and deletions - a minimum of 90% of reads agreeing with the indel.